During the past ten years, Ausubel lab has pioneered the isolation and characterization of Arabidopsis enhanced disease susceptibility (eds) mutants by direct screening, the first time that innate immunity had been subjected to rigorous and systematic genetic analysis in any eukaryotic organism. This work, as well as work from other labs, identified a variety of innate immune response pathways that regulate a multi-faceted immune response using salicylic acid (SA), jasmonic acid (JA), or ethylene (ET) as secondary messengers. Our primary goal, is to identify defense-related pathways that function in parallel (or that intersect with) the previously identified SA, JA, and ET pathways. Specifically, we have produced a substantial body of both published work and preliminary results concerning signaling pathways that respond to a highly conserved 22 amino acid bacterial flagellar peptide called Flg22. An important unanswered question in the plant innate immunity field is how the Flg22 pathway and other similar pathways that respond to so-called non-specific microbe associated molecular patterns (MAMPs) are related to the SA and JA/ET signaling pathways that primarily respond to pathogen-specific signals. We are currently using multiple approaches to further investigate this problem.

For example, we used transcriptional and metabolic profiling in Arabidopsis T-DNA mutants, coupled with the monitoring of pathogen triggered callose deposition, to identify major roles in the response to Flg22 for the plant hormone ethylene and the secondary metabolite 4-methoxy-indol-3-ylmethylglucosinolate. This study showed that the well-studied glucosinolates, previously shown to be important in avoiding damage by herbivores, are also required as a component of the plant defense response against microbial pathogens.

In another study, by monitoring transcriptional activation of GUS reporters and MAMP-elicited callose deposition, we showed that three MAMPs, Flg22, peptidoglycan, and chitin trigger a strong tissue-specific response in Arabidopsis roots, either at the elongation zone for Flg22 and peptidoglycan, or in the mature parts of the roots for chitin. Ethylene signaling, the 4-methoxy-indole-3-ylmethylglucosinolate biosynthetic pathway, and the PEN2 myrosinase, but not salicylic acid or jasmonic acid signaling, play major roles in this MAMP response. We also showed that Flg22 induces the exudation of the well-studied phytoalexin camalexin by Arabidopsis roots dependent on the cytochrome P450 CYP71A12 at physiologically significant concentrations. Interestingly, we also showed that the pathogenic bacterium Pseudomonas syringae and the beneficial microbe Pseudomonas fluorescens suppress the MAMP response in roots via the secretion of the phytotoxin coronatine, an isoleucine-jasmonic acid mimic, in the case of P. syringae, and via an unknown mechanism for P. fluorescens. The coronatine–mediated suppression of MAMP responses, including transcription of MYB51, a transcription factor involved in MAMP signaling pathways, requires the E3 ubiquitin ligase COI1 and the transcription factor JIN1/MYC2, but does not rely on salicylic acid-jasmonic acid antagonism. These latter experiments demonstrate the presence of highly orchestrated and tissue-specific MAMP responses in roots and pathogen-encoded mechanisms to block these MAMP-elicited signaling pathways.

A final Arabidopsis project concerns the underlying mechanisms by which P. aeruginosa and P. syringae are able to infect Arabidopsis leaves. In the case of P. aeruginosa, we have found that the disaccharide trehalose is a key P. aeruginosa virulence factor. We are currently testing several hypotheses concerning the role of trehalose in the infection process, including the extraction of nutrients from plant cells. Interestingly, the ability to extract nutrients from mesophyll cells is also a key factor underlying P. syringae virulence. Conversely, we have discovered that the withdrawal of nutrients from the intercellular spaces in the leaf, especially amino acids, is an important Arabidopsis defense response to pathogen attack.